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################################################################################
# Copyright 2011
# Andrew Redd
# 11/23/2011
#
# Description of File:
# Makefile for knitr compiling
# 
################################################################################
all:pdf  # default rule DO NOT EDIT

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This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown) 
using [knitr](http://yihui.name/knitr/) in Rstudio 0.96.
This combination of tools provides an exciting improvement in usability for 
[reproducible analysis](http://stats.stackexchange.com/a/15006/183).
Specifically, this post 
(1) discusses getting started with R Markdown and `knitr` in  Rstudio 0.96;
(2) provides a basic example of producing console output and plots using R Markdown;
(3) highlights several code chunk options such as caching and controlling how input and output is displayed;
(4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and 
(5) discusses the implications of R Markdown.

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#!/usr/bin/env python
# split a bam file by read group ID
# Sean Davis <seandavi@gmail.com>
# March 10, 2012
# 
import pysam
import argparse
import logging

logging.basicConfig(level=logging.INFO)

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# Read .mp3 files from a given directory, compare songs, and play them in order of similarity
# To run, source this file, then:
# arrangeMusicC(inDirectory = getwd())

library("plyr")
library("tuneR")
library("seewave")

library("compiler")

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library("igraph")
rm(list = ls())
##########################################################################
# Read data
dataSet <- read.table("http://www.vesnam.com/Rblog/wp-content/uploads/2013/07/lesmis.txt",
                      header = FALSE, sep = "\t")

# Create a graph. Use simplify to ensure that there are no duplicated edges or self loops
gD <- simplify(graph.data.frame(dataSet, directed=FALSE))

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library("igraph")
library("plyr")
library("HiveR")
library("RColorBrewer")
library("grDevices")

############################################################################################
rm(list = ls())

dataSet <- read.table("http://www.vesnam.com/Rblog/wp-content/uploads/2013/07/lesmis.txt",

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dual_dendogram_tile_plot <- function(data.matrix, main="Title"){

#Dual dendrogram ############

x <- data.matrix
dd.col <- as.dendrogram(hclust(method="ward",dist(x)))
col.ord <- order.dendrogram(dd.col)

dd.row <- as.dendrogram(hclust(method="ward",dist(t(x))))
row.ord <- order.dendrogram(dd.row)

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#####
## AUTHOR: BRIAN M. BOT
## ORGANIZATION: SAGE BIONETWORKS
##
## ALLOW USERS TO LEVERAGE KNITR WHEN CONSTRUCTING SYNAPSE WIKI CONTENT
#####
## PARAMETERS:
##   file: path to a local .Rmd file which to knit
##   owner: a Synapse object which will own the resulting WikiPage (usually a Project, Folder, or File)
##   parentWikiId (optional): if the resulting WikiPage is to be a subpage of another WikiPage, this is the id for the parent WikiPage (NOTE: owner is still required)

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# Note: using the devel versions of both packages!
library(DESeq) # version 1.9.11
library(edgeR) # version 2.99.8
library(VennDiagram)

# Read in data ------------------------------------------------------------

## Use pasilla data
datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
datafile

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// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console